Many Muslim Arabs think of the Pakistan v. India issue as one of a minority foreign Muslim invader taking over Hindu lands with Hindu majorities. They regard this as the same as a minority foreign Jewish invader taking over Arab lands. I am not going to comment on whether this view is right or not. Just pointing out this is their view.
As far as the Jewish population of Israel is concerned, half of them came from Europe. However, more than 80% of European Jews still retain Middle/ Near Eastern paternal ancestry. So, it would not be fair to say the majority of them have European paternal ancestry.
As far as the Muslims of India and Pakistan are concerned, most of them are Hindu converts not descendants of foreigners, Muslim or otherwise. The only exception are the Shia of Northern India, specifically, Uttar Pradesh, who have a significant percentage of Iranian/ Central Asian paternal ancestry.
regards,
bob